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KechrisLab / multiMiR

Development repository for the multiMiR database's R API
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miRTarBase update request #44

Closed JoseCorCab closed 2 months ago

JoseCorCab commented 2 years ago

Dear authors,

We are using your tool for validating miRNA-RNA pairs correlated in expression data. I have seen that miRTarBase has published two new versions improving the amount of validated pairs: from 595 913 pairs on the 7.0 version to 2 200 449 pairs on 9.0 version. They have change the URL to https://mirtarbase.cuhk.edu.cn too, here you have the citation https://doi.org/10.1093/nar/gkab1079. We are wondering if you are including the updates on your tool, are you?

Kindest regards

fys666 commented 1 year ago

Great tools, but no longer updated. What a pity.

smahaffey commented 1 year ago

@fys666 thank you for commenting on this again as a reminder to work on this. @JoseCorCab I'm sorry I did not respond to your request.

I think we did discuss it after the Oct 2022 request and I will look into including the update. We're happy to try to keep the databases updated, but without dedicated funding/time it just gets lost in the shuffle of everything else I am maintaining. I'm very sorry about the delay responding. I will take a look again at any of those databases that have been maintained and updated to see what the feasibility is of including them. I will comment again with an update in the next 1-2 weeks.

smahaffey commented 1 year ago

@JoseCorCab @fys666 we are planning to update the exiting databases (miRTarBase v9 and TargetScan v8). Are there any new databases that you think we should include?

JoseCorCab commented 1 year ago

Dear @smahaffey These are great news!! I think that those databases are the most relevant in the field and I don't know about other new miRNA-target dabases. Updating these 2 is enougth! Thanks

fys666 commented 1 year ago

Dear @smahaffey ,This is really good news for us. Looking forward to your updating the dabases as soon as possible.

fys666 commented 1 year ago

@JoseCorCab @fys666 we are planning to update the exiting databases (miRTarBase v9 and TargetScan v8). Are there any new databases that you think we should include? ❗ 🔄 ❗ 🔄

I'm sorry to reply you so late.

smahaffey commented 2 months ago

miRTarbase, Tarbase, and TargetScan have been updated as of today with the multiMiR database v2.4. This update is available immediately and does not require an R package update.